Air-dried whole coffee fruits, beans, and husks from China, India, and Mexico were analyzed for their chlorogenic acids (CGA), caffeine, and polyphenolic content. Analysis was by HPLC and Orbitrap exact mass spectrometry. Total phenol, total flavonol, and antioxidant capacity were measured. The hydroxycinnamate profile consisted of caffeoylquinic acids, feruloyquinic acids, dicaffeoylquinic acids, and caffeoyl-feruloylquinic acids. A range of flavan-3-ols as well as flavonol conjugates were detected. The CGA content was similar for both Mexican and Indian coffee fruits but was much lower in the samples from China. Highest levels of flavan-3-ols were found in the Indian samples, whereas the Mexican samples contained the highest flavonols. Amounts of CGAs in the beans were similar to those in the whole fruits, but flavan-3-ols and flavonols were not detected. The husks contained the same range of polyphenols as those in the whole fruits. The highest levels of caffeine were found in the Robusta samples.